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* Add precision to printed PIC parameters
* Added WarpX_PARTICLE_PRECISION as a build option
* Update types to ParticleReal
* Updated libwarpx to inject particles with correct ParticleReal type
* Fix syntax error
* Add logic to avoid duplicate definitions
* Use correct ParticleReal type in add_particles
* Cleaned up code, addressed comments
* Update Python/pywarpx/_libwarpx.py
Co-authored-by: Peter Scherpelz <31747262+peterscherpelz@users.noreply.github.com>
* Removed redundant functions, fixed some typing
* Modified template functions
* Cast d_w to Real
* Fixed failing tests
* Cast types to be consistent
* removed in-tree-build from pip command
* Added GPU device macros to PDim3 methods
* rerun tests
* Removed unecessary casting, update calls to use PDim3 instead of XDim3
* Refactored comments
* Added mcc fields double precision, particles single precision test
* Updated casting and formatting
* Removed cast, updated declaration
Co-authored-by: Peter Scherpelz <peter.scherpelz@modernelectron.com>
Co-authored-by: Peter Scherpelz <31747262+peterscherpelz@users.noreply.github.com>
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* Add Headers to Input File Written by PICMI
* Commit Suggestion by @dpgrote
* Add Comment
* Add Empty Line
* Slightly Better Readable with a newline
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* Added STL files support in pywarpx
* Add new EB bucket
* Added name to file headers
* Fixing year in file headers
* Checking that stl file and imp function are not both specified
* Renamed EB bucket to EB2
* Adding STL documentation
* Implement suggestions from code review
Co-authored-by: lgiacome <lorenzo.giacome@cern.ch>
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* Added PlasmaLens class to PICMI
* Added CI test
* Added PICMI input file
* Fixed the output dir for the CI test
* Add `_plt` to Output File Prefix
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Beginnings of signal handling machinery
* Add tentative logic to make checkpoint call
* Adapt formatting slightly
* Add calls to read signals and set up signal handlers
* Initialize signal flag array
* Add parsing of signal names, and fix some whitespace issues
* Skip signal setup on Windows
* added checkpoint and break signal inputs to picmi.py
* Address initial review requests
* Correct comment to match changed code
* Convert maximum signal number to a symbolic name
* Always parse signal input, and error out on Windows or wherever it may be unsupported
* Typo fix
* Add missing reset of checkpoint signal flag
* Add reset of break signal, in support of Python or library usage
* Test for a configured checkpoint diag when asked to checkpoint on a signal
* Fix typo in Linux code path
* Clean up MPI support
* Use symbolic name for maximum signal number
* Fix unused variable in the no-MPI case
* Add missing header inclusions
* Switch signal parsing to an enumerated table
* Test signal handling for Linux, not GNU C library
* Avoid another magic number
* Update MPI_Ibcast call to match symbolic array length
* Update loop over signal flags to use symbolic limit
* Match #includes to usage
* Add omitted C++ std <atomic> header include
* Guard entire set of signal definitions as *nix-only, not for Windows
* Broaden Windows exclusion to avoid zero-length array that displeases MSVC++
* Check return value from sigaction()
* Convert conditional calls to Abort() to assertions
* Move check for platform support to input parsing
* Shift signal handling code over toward ABLASTR to share with ImpactX and Hipace++
* Minor cleanup
* A bit more cleanup
* Fix formatting nits
* Add AMReX error handling on MPI calls
* Add ABLASTR signal handling code to GNU makefile too
* Document new input parameters
* Use ABLASTR assertion macros in ABLASTR code
* Convert requests limit value to a requests array size
* Generalize signal handling to an arbitrary set of potential actions
* Rename class to match usage and file name
* Stick stuff in ABLASTR namespace
* Indent conditional includes as requested
Co-authored-by: Roelof <roelof.groenewald@modernelectron.com>
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* Rename `serialize_ics` as `serialize_initial_conditions`
* Add Backward Compatibility Check
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Add for all diagnostics the equivalent of `<diag>.file_min_digits`.
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* added Coulomb collision installation to picmi.py
* added comment saying the input values for the new PICMI test comes from inputs_2d
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zero particles (#2808)
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* add python callbacks before and after collisions
* re-order callback declarations
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* add SyncRho call to warpx_depositChargeDensity
* expose SyncRho to Python; add warpx_clearChargeDensity to reset rho_fp before deposition
* remove unneeded warpx_clearChargeDensity function
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* add (default) option to depositChargeDensity to call SyncRho after deposition
* added option to depositChargeDensity to zero out rho_fp before deposition
* code cleanup
* import fields from inside depositChargeDensity
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* added python wrapper function to deposit a specific species density in rho_fp
* added 1D ES input file with MCC that uses the charge deposition functionality
* reset rho_fp[lev] before depositing
* updated documentation
* switch to using simulation.extension in Poisson solver
* Apply suggestion from code review
Co-authored-by: Phil Miller <phil.miller@intensecomputing.com>
* suggested changes from code review
* add comment explaining why a direct Poisson solver is used
* removed direct solver in 1D example since it is actually slower than the MLMG solver
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* added docstring for warpx_depositChargeDensity
* fixed order of imports in new PICMI input file
Co-authored-by: Phil Miller <phil.miller@intensecomputing.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* added support to uninstall an external Poisson solver and return to using the default MLMG solver; also updated some callbacks.py calls to Python3
* refactor callback handling - use a map to handle all the different callbacks
* warpx_callback_py_map does not need to link to C
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* further suggested changes from code review
* added function ExecutePythonCallback to reduce code duplication
* moved ExecutePythonCallback to WarpX_py
* added function IsPythonCallbackInstalled
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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Trying to fix the macOS PyPy 3.7 error seen in https://github.com/conda-forge/warpx-feedstock/issues/37
Testing in https://github.com/conda-forge/warpx-feedstock/pull/38
After googling for a while, the original implementation was likely based on https://code.activestate.com/lists/python-list/704158, which contains bugs.
1) Bug: `create_string_buffer`
Allocating new, null-terminated char arrays with `ctypes.create_string_buffer` does lead to scrambled arrays in pypy3.7.
As far as I can see, this [should have also worked](https://docs.python.org/3/library/ctypes.html), but maybe there is a bug in the upstream implementation or the original code created some kind of use-after-free on a temporary while the new implementation just shares the existing byte address.
This leads to errors such as the ones here:
https://github.com/conda-forge/warpx-feedstock/pull/38#issuecomment-1010160519
The call `argvC[i] = ctypes.c_char_p(enc_arg)` is equivalent in creating a `NULL`-terminated char array.
2) Bug: Last Argv Argument
The last argument in the array of char arrays `argv` in ANSII C needs to be a plain `NULL` ptr.
Before this PR, this has been allocated but never initialized, leading to undefined behavior (read as: crashes).
Reference: https://stackoverflow.com/a/39096006/2719194
3) Cleanup: there is a pre-defined `ctypes.c_char_p` we can use for pointer of char.
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* Set geometry earlier in Python
* Fix comment typos
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* Make moving window dimensionality consistent in PICMI
* update PICMI_inputs_plasma_acceleration_1d.py
* two elements for moving window velocity in RZ
* update RZ laser_acceration test
* update PICMI version
* update PICMI Langmuir RZ test
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* allow Dirichlet BCs in r when r_min != 0 with ES RZ simulations
* handle the rmax boundary condition setting properly when rmin == 0
* add ability to specify rmin and rmax potentials through picmi
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* Initial attempt at moving function into LibWarpX
* Bugfix - undefined structs in get_particle_theta
This is untested, identified by IDE/visual inspection only
* Unify newlines
* Delete libwarpx.clight (duplicated picmi.py)
See picmi.constants.c
* Change function descriptive comment to docstring
Also remove extra newline in __init__ beginning.
* Replace pywarpx/_libwarpx calls appropriately
* Fix atexit register of finalize function
* Reorder WarpX.py imports for pre-commit
* Use picmi.Simulation.extension = libwarpx alias
This will hopefully preempt user script changes if we restructure things
to allow multiple WarpX runs to be done within a single Python script.
* Fix libwarpx ref in WarpX.getProbLo/getProbHi
* Update get_particle_boundary_buffer doc reference
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* pre-commit: Python imports
Add two new Python rules to:
- remove unused imports
- sort imports according to PEP8
* pre-commit: Python imports
Add two new Python rules to:
- remove unused imports
- sort imports according to PEP8
`.editorconfig`: isort options
https://github.com/PyCQA/isort/wiki/isort-Settings
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* move import os (mpl)
* move import yt (mpl)
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Cleanup around matplotlib.use
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Cleaning: double np and lib
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* Docs: `geometry.dims` option
Add a new, required option to specify the geometry of an
inputs file at runtime.
* Check & Report Runtime Dims Mismatch
* Examples: add `geometry.dims`
* Deprecation Warning: `geometry.coord_sys`
* PICMI: `geometry.dims`
* Improve error message
sounds a bit better
* Improve Doc Description
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
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* Wrap shared object in a class to control its loading
* Fix libwarpx attribute references
* Updated callbacks.py for updated libwarpx
* Removed the wx module plus other clean up
* Further revision of how to use the pywarpx module.
Now, _libwarpx should not be imported by external scripts except in special circumstances.
* Updated documentation
* Clean up end of line whitespace
* Added more wrapping routines plus some clean up
* Fixed use of pywarpx in two examples
* Fix for getistep
* Fixed for the EB Python interface
* Silence a warning for our wrapper
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Adding edge_lengths and face_areas to the Python interface
* Added wrappers for the two new arrays of data
* Adding a CI test
* Fixed test name
* Added customRunCmd
* Added mpi in test
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* modify requirements.txt and add input file for 1D Python pwfa
* add 1D Python plasma acceleration test to CI
* picmi version
* USE_PSATD=OFF for 1D
* Update Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration_1d.py
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Regression/WarpX-tests.ini
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Cartesian1D class in pywarpx/picmi.py
* requirements.txt: update picmistandard
* update picmi version
* requirements.txt: revert unintended changes
* 1D Laser Acceleration Test
* Update Examples/Physics_applications/laser_acceleration/inputs_1d
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration_1d.py
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* add data_list to PICMI laser_acceleration test
* increase max steps and fix bug in pywarpx/picmi.py 1DCartesian moving window direction
* add data_lust to Python laser acceleration test
* picmistandard update
Co-authored-by: Prabhat Kumar <prabhatkumar@kraken.dhcp.lbl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* added _getitem1d and _setitem1d to fields.py
* refactored fields.py to reduce duplicate code for different dimensions
* fixed some bugs with the refactor
* changes requested during code review
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* Added check for if warpx was initialized when calling finalize
* Renamed to be warpx_initialized
* Fixed reference to global variable
Co-authored-by: Peter Scherpelz <31747262+peterscherpelz@users.noreply.github.com>
* Changed global variable to member of libwarpx
* Fixed syntax errors
* Remove custom arg from argv to avoid parmparse error
Co-authored-by: Peter Scherpelz <31747262+peterscherpelz@users.noreply.github.com>
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* Python: Start 1D Support
Start supporting 1D builds in Python.
* Fix 1D: PML FillZero unused
... since PMLs are not yet supported in 1D.
* BeamRelevant: Fix unused p_pos0
* FromTXYEFileLaserProfile: Not Impl in 1D
* QED Schwinger: 1D not Implemented
Fix unused warnings, add aborts.
* 1D RealVect/IntVect: Initialization
Use explicit scalar constructors, no braces.
Fix warning in clang 10.
* 1D NCI Filter: Fix unused members & Init
Unimplemented, but throws warnings.
* PSATD: 1D not Implemented
- remove compile warnings
- start porting some parts
* NCIGodfreyFilter: Clean up 2D & Else
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* Python: More Nullptr Checks
I am debugging a couple of crashes while mitigating CI.
One of them pointed to the locations here
(`ValueError: NULL pointer access`), so I decided to add some checks.
* Skip invalid tiles
* Skip Empty Tiles But Check Pointer
* Python: nullptr check in _array1d_from_pointer
Make the methods `get_particle_structs` and
`get_particle_boundary_buffer_structs` more robust.
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* Add pre-commit
Add basis for automated pre-commit checks.
Install locally via:
```bash
python3 -m pip install -U pre-commit
pre-commit install
```
See: https://pre-commit.com
* Cleanup: Whitespaces
* Cleanup: requirements.txt order
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buffers (#2498)
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* PICMI: Add amr.max_grid_size_<x,y,z>
* Set All Flags in Python
* PICMI: Add amr.blocking_factor_<x,y,z>
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* Add Python Wrappers for F,G in PML
* Add Getters for F,G Nodal Flags
* Fix Bug in <F,G>FPPMLWrapper (Default Level)
* Fix Bug in F,G Nodal Flags
* Use GetPML Method for F,G Nodal Flags
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* added option to specify absolute tolerance for the MLMG solver used in the electrostatic field solve
* added absolute tolerance argument to the documentation
* fixed bug introduced during copy and paste
* expanded documentation for MLMG solver absolute tolerance (added unit) and added a link to the AMReX documentation describing the MLMG solver parameters
* possibly more robust handling of the MLMG convergence
* switched from std::max to amrex::max to hopefully fix compiler complaints
* updated checksum values for MCC test (background_mcc); the values changed only slightly, presumably due to a difference in the initial field solve which would now have the absolute tolerance value included, but since the Python version of this same test (which uses the direct solver) still passes the change is assumed to be inconsequential
* another try to fix the compile issues
* print a message to notify user if the max norm of rho is zero
* Apply suggestions from code review
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* switched print statements to the new warning logger
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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Fixed indexing for PML fields.
Add all of the fixes to the setitems routines.
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* PICMI: Add div(E),div(B) Cleaning Options
* Update PICMI Version: 0.0.15
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* Fix fields indexing
* Added additional documentation
* Fixed comment
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Kevin Z. Zhu
Edoardo Zoni
Lorenzo Giacomel
Roelof Groenewald
David Grote
Phil Miller
David Grote
Ryan Sandberg
Axel Huebl
Prabhat Kumar
Peter Scherpelz
